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Crystal Strucuture of The Berberine-bound Form of RamR (Transcriptional Regurator of TetR Family) from Salmonella Typhimurium
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1M MES, 20mM NaPi, 75mM NaCl, 0.2M Ammonium sulfate, 2mM DTT, 20% PEG 6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.4 48.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.817 α = 104.97 b = 54.623 β = 97.74 c = 92.291 γ = 90.04
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX225HE 2012-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.34 50 95.1 0.075 11.3 3.2 32813
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.39 90.9 0.41 3.6 1545
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.34 41.29 32793 1693 94.62 0.2266 0.2248 0.2212 0.261 0.2544 RANDOM 53.5272
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.12 0.02 -0.03 0.09 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.52 r_dihedral_angle_4_deg 18.848 r_dihedral_angle_3_deg 15.956 r_scangle_it 5.424 r_dihedral_angle_1_deg 4.375 r_scbond_it 3.596 r_mcangle_it 2.699 r_angle_refined_deg 1.746 r_mcbond_it 1.512 r_chiral_restr 0.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.52 r_dihedral_angle_4_deg 18.848 r_dihedral_angle_3_deg 15.956 r_scangle_it 5.424 r_dihedral_angle_1_deg 4.375 r_scbond_it 3.596 r_mcangle_it 2.699 r_angle_refined_deg 1.746 r_mcbond_it 1.512 r_chiral_restr 0.134 r_bond_refined_d 0.024 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5845 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 120
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling